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Simulating the Capture and Translocation of Rigid fd Viruses though a Nanopore
Hendrick de Hann University of Ontario Institute of Technology
PIRSA:14050036 -
Recent advances in the search for complementary sequences
Ilias Kotsireas Wilfrid Laurier University
PIRSA:14050040 -
Frozen Spin Ice Ground States in the Pyrochlore Magnet Tb2 Ti2 O7
Bruce Gaulin Canadian Association of Physicists
PIRSA:14050019 -
Measurements of Noice in Condensed Matter Systems Using Superconducting Qubits and Resonators
Adrian Lupascu Institute for Quantum Computing (IQC)
PIRSA:14050018 -
Strain Induces Helical Flat Band & Interface Superconductivity in Topological Crystalline Insulators
Evelyn Tang Rice University
PIRSA:14050017 -
Using β-NMR to Solve Hard Problems in Soft Condensed Matter
James Forrest University of Waterloo
PIRSA:14050023 -
Generic Spin Model for Honeycomb Iridates Beyond the Kitaev Limit
Jeffrey Rau University of Toronto
PIRSA:14050025
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Modelling Surface Driven Flows in the Ocean
Eric Bembenek University of Waterloo
PIRSA:14050047Buoyancy driven flows at the top of the ocean or bottom of the atmosphere are inherently different from their interior dynamics. Oneidealized model that has recently become very popular to idealizethese surface flows with strong rotation is Surface Quasi-Geostrophic (SQG) dynamics. This model is appropriate for large-scale dynamics and assumes the motion is in near geostrophic and hydrostatic balance. Many of the numerical simulations of SQG have shown thatvortices are frequently generated at very small scales scales thatare well beyond the SQG limits.In this talk we examine the dynamics of a rotating three-dimensionalelliptic vortex in both the SQG model and a more general and muchmore complicated primitive equation model. In order to compute highresolution solutions to the three dimensional primitive equations we make use of Sharcnet resources. We find that in the case of strongrotation (small Rossby number) we confirm the predictions from SQG.With weaker rotation (moderate Rossby number) we see the non-SQG effects that arise and find that the regime where SQG can beappropriate can be very limited. We conclude that some of thepredictions that arise from the SQG model might not be very accuratein idealizing geophysical flows at the surface. -
Biological graph dissimilarity characterization using graph theory
PIRSA:14050043Many biological data sets and relationships can be modeled as graphs. Understanding how structure of these graphs relates to biological function is essential for understanding underlining mechanisms of disease and for aiding drug discoveries. Vertices of biological graphs represent individual entities such as genes and proteins. Edges represent the relationship between two cellular components such as physical and functional interactions. A challenging problem in the post-genomic era is graph comparisons as they are large typed complex and evolving. Comparing graph structures helps to gain insights into the underlying signaling mechanisms and treatments for complex diseases. With technological advancement biological data will continue to grow and so will the size and complexity of graphs.Large graph comparisons are computationally intensive as they involve the subgraph isomorphism problem which is NP-complete. Therefore graph comparison algorithms need to be efficient scalable and be able to systematically capture biologically meaningful graph structure differences. Efficient graph comparison algorithms are necessary for many types of biological graphs e.g. protein-protein interaction drug-target microRNA-gene gene-regulatory and co-expression graphs. Furthermore graph comparison algorithms are extremely useful for many applications such as comparing graphs characterizing different diseases representing different cancer subtypes or different drug treatment responses. There are two main categories of graph properties used for comparing biological graphs global graph properties and local graph properties. Global graph properties study the overall graph while local graph properties focus on local structures of the graph. Our objective is to develop an efficient scalable graph comparison algorithm such that graph structure differences between any two states can be obtained systematically. We achieve the objective in two steps. First we propose an algorithm such that graph structure differences are systematically obtained and verified that the differences are biologically meaningful. Then we develop a heuristic to improve upon the proposed algorithm in the first step in terms of efficiency and scalability. While our approaches are generic we apply it on non-small cell lung cancer data sets. The non-small cell lung cancer datasets are used to construct normal and tumor co-expression graphs. Global graphs properties do not contain the detail needed to capture the structural characteristics of biological graphs thus we used a local property graphlets. Graphlets are all non-isomorphic connected induced graphs on a specific number of vertices. By definition graphlets have the ability to capture all the local structures on a certain number of vertices. Results showed that our graphlet approach returns graph structure differences between normal and tumor conditions that correspond to biological knowledge. We then introduce a heuristic to identify areas that are likely to be different between the normal and tumor graph and perform graph comparisons on the identified areas only. The heuristic was able to achieve interesting results that were successfully validated in vitro. -
HPC Application in Large Eddy Simulation of Fuel Spray / Air Jet interaction
PIRSA:14050046Along with the development of computational resources computational fluid dynamics (CFD) has evolved in resolving the finest length scales and smallest time scales of the flow. Direct numerical simulation (DNS) resolves the finest flow scales known as Kolmogorov length scales which are responsible for the dissipation of the energy transferred from the large and intermediate length scales. However DNS simulations are computationally costly and demand very powerful resources which are not widely available to this day. Large eddy simulation (LES) is a more feasible tool to resolve the large flow scales and model the sub-grid scales using a Reynolds averaged modeling. High performance computing tools make it possible to perform high fidelity large eddy simulations which reasonably (almost twelve times the Kolmogorov length scale) resolve the flow structures.In the present study large eddy simulation is utilized to simulate interaction of a high speed compressible round air jet with a group of sprays injected from a six-hole nozzle injector into the shear layer of the air jet. Fuel sprays are injected with 10 and 15 MPa injection pressures in the jet cross flows of 125 and 215 m/s. Simulations are performed using 64 processors and 240 GB of memory. The focus of the study is on the spray atomization assisted by air jet cross-flow. Consequent processes of fuel/air mixing are also investigated by focusing on the role of vortical structures resolved using large eddy simulation. -
Solving initial-boundary value problems without numerical differentiation
PIRSA:14050042The numerical solution of nonlinear partial differential equations with nontrivial boundary conditions is central to many areas of modelling. When high accuracy is required (pseudo) spectral methods are usually the first choice. Typically in this approach we search for the pre-image under a linear operator which represents a combination of spatial derivatives along with the boundayr conditions in every time step. This operator can be quite ill-conditioned. On a basis of Chebyshev polynomials for instance the condition number increases algebraically with the number of basis functions. I will present an alternative method based on recent work by Viswanath and Tobasco which avoids numerical differentiation entirely through the use of Green's functions. I will demonstrate this method on the Kuramoto-Sivashinsky equation with fixed boundary conditions. -
New insights into polymer-induced drag reduction in turbulent flows
PIRSA:14050041Polymer additives are known to cause significant reduction in turbulent friction drag and reduce the energy dissipation rate of fluid transport. This effect is however bounded by a universal upper limit the maximum drag reduction (MDR) asymptote that does not change with polymer properties. Understanding MDR remains an important unsolved problem in the areas of turbulence and non-Newtonian fluid mechanics. Dynamical trajectories on the boundary in state space between laminar and turbulent plane channel flow - edge states - are computed for Newtonian and viscoelastic fluids. Viscoelasticity has a negligible effect on the properties of these solutions and at least at a low Reynolds number their mean velocity profiles correspond closely to experimental observations for polymer solutions in the MDR regime. These results confirm the existence of weak turbulence states that cannot be suppressed by polymer additives explaining the fact that there is an upper limit for polymer-induced drag reduction. -
Simulating the Capture and Translocation of Rigid fd Viruses though a Nanopore
Hendrick de Hann University of Ontario Institute of Technology
PIRSA:14050036The passage of long biological molecules from one side of a membrane to the other through a nanoscale hole has been the subject of intense research in recent years. Motivated by the possibility of new sequencing technologies the focus of this work has been studying the translocation of DNA across biological and synthetic membranes. In this talk I will present results from a joint experimental-simulation study examining the translocation of rod-like fd viruses through a nanopore. While DNA is relatively flexible the fd virus has a persistence length that is over twice that of its contour length and is thus stiff. In principle translocation in this rod-like limit is much easier to model. However I will show that experimental results for the distribution of translocation times exhibit significant deviations from the expected result. I will present a model for fd translocation that was developed to probe these results. Simulations based on this model yield insight into previously unclear experimental results including i) details of how the polymer is capture by the pore at different external fields ii) a correlation between the translocation time and the conformation at capture and iii) sources for the increased dispersion in the translocation time distributions. -
Recent advances in the search for complementary sequences
Ilias Kotsireas Wilfrid Laurier University
PIRSA:14050040We will present recent developments in the search for complementary sequences namely new theoretical and algorithmic progress. SHARCNET resources are used quite heavily in this project. -
Frozen Spin Ice Ground States in the Pyrochlore Magnet Tb2 Ti2 O7
Bruce Gaulin Canadian Association of Physicists
PIRSA:14050019Tb2Ti2O7 was one of the first pyrochlore magnets to be studied as a candidate for a spin liquid or cooperative paramagnet, and its ground state has remained enigmatic for fifteen years. Recent time-of-flight neutron scattering studies have shown that it enters a glassy Spin Ice ground state, characterized by frozen short range order over about 8 conventional unit cells, and the formation of a ~ 0.08 meV gap in its spin excitation spectrum at the appropriate quasi-Bragg wave vectors. I will introduce the relevant Spin Ice physics background, and describe how the experiments are performed. The new H-T phase diagram for Tb2Ti2O7 in a [110] magnetic field will be presented. This shows that its frozen (i.e. glassy) Spin Ice ground state (at low temperature and zero field) and its conventional field-induced ordered phase (at low temperature and high fields) bracket the cooperative paramagnetic phase which generated the original interest in this fascinating magnet. -
Measurements of Noice in Condensed Matter Systems Using Superconducting Qubits and Resonators
Adrian Lupascu Institute for Quantum Computing (IQC)
PIRSA:14050018Superconducting qubits based on Josephson junctions and resonators are presently leading candidates for the implementation of quantum computing. These systems couple strongly to their environment, which often makes preservation of coherence challenging. This strong coupling can be turned into an advantage: it enables the investigation of noise and loss at low temperatures. I will discuss two topics. The first topic is the use of superconducting flux qubits to measure magnetic flux noise. The second topic is the measurement of microwave loss in amorphous dielectric materials. Experiments with superconducting coherent systems can be used to extract new information on flux noise and dielectric loss, not accessible using other methods used in the past, providing useful input to theoretical developments. -
Strain Induces Helical Flat Band & Interface Superconductivity in Topological Crystalline Insulators
Evelyn Tang Rice University
PIRSA:14050017Topological crystalline insulators in IV-VI compounds host novel topological surface states, that at low energy, consist of multi-valley massless Dirac fermions. We show that strain generically acts as an effective gauge field on these Dirac fermion surface states and creates pseudo-Landau orbitals without breaking time-reversal symmetry. We predict this is naturally realized in IV-VI semiconductor heterostructures due to the spontaneous formation of a misfit dislocation array at the interface, where the zero-energy Landau orbitals form a nearly flat band. We propose that the high density of states of this topological flat band gives rise to the experimentally observed interface superconductivity in IV-VI semiconductor multilayers at temperatures that are unusually high for semiconductors, and explains its non-BCS dependence on dislocation array period. -
Using β-NMR to Solve Hard Problems in Soft Condensed Matter
James Forrest University of Waterloo
PIRSA:14050023Beta-detected nuclear spin relaxation of 8Li+ has been used to study important problems in polymer physics. In the first case we probe the depth dependence of molecular dynamics in high- and low-molecular-weight deuterated polystyrene (PS-d8). The average nuclear spin-lattice relaxation rate, 1/T1 avg, is a measure of the spectral density of the polymer dynamics at the Larmor frequency (41MHz at 6.55Tesla). The mean fluctuation rate decreases approximately exponentially with distance from the free surface, returning to bulk behavior for depths greater than ~10nm and the effective thickness of the surface region increases with increasing temperature. These results present challenges for the current understanding of dynamics near the free surface of polymer glasses. In the second case, we use the technique to make the first quantitative measurements of surface segregation in samples that are blends of two chemically identical polymers with different degrees of polymerization. -
Generic Spin Model for Honeycomb Iridates Beyond the Kitaev Limit
Jeffrey Rau University of Toronto
PIRSA:14050025Recently, realizations of Kitaev physics have been sought in the A2IrO3 family of honeycomb iridates, originating from oxygen-mediated exchange through edge-shared octahedra. However, for the J=1/2 Mott insulator in these materials exchange from direct d-orbital overlap is relevant, and it was proposed that a Heisenberg term should be added to the Kitaev model. Here we provide the generic nearest-neighbour spin Hamiltonian when both oxygen-mediated and direct overlap are present, containing a bond dependent off-diagonal exchange in addition to Heisenberg and Kitaev terms. We analyze this complete model using a combination of classical techniques and exact diagonalization. Near the Kitaev limit, we find new magnetic phases, 120 degree and incommensurate spiral order, as well as extended regions of zigzag and stripy order. Possible applications to Na2IrO3 and Li2IrO3 are discussed.